Genetic homogeneity is the basic demand for an inbred strain of laboratory animal, which could be detected in multi-levels, including morphology, cytogenetics, biochemistry, immunogenetics, molecular genetics and so on. Biochemical markers and skin grafting were recommended methods for genetic quality control of mammalian animals in the national standard GB14923-2001. However, no prescriptive methods were destined for monitoring genetic quality of aquatic laboratory animals. Gobiocypris rarus is an endemic cyprinid fish in China, distributed only in Sichuan Province. Because this species has many attractive attributes, including sensitivity to chemicals, small size, eurythermal, easily to be cared in laboratory, short life cycle ( about 4 months) and so on, it has been widely used in mail),, researches of fish pathology, genetics, toxicology, embryology, and physiology in China. An inbred strain of Gobiocypris rarus, named HAN strain, has been, established by brother-sister mating to the 23rd generation in the laboratory since 1990. In order to investigate the genetic background of the HAN strain and to monitor its genetic quality, we examined the inbred strain on external morphometric and meristic characters, skeletal morphometrics, survival of scale transplantation, electropherogram of isozymes and microsatellite polymorphism. The present study was a part of these series works on the examination of molecular genetic homogeneity. A total of 17 microsatellite markers were used to analyze on 30 individuals of F22, 20 individuals of F20 of the HAN strain in contrast with 30 individuals of wild type which were caught in Hanyuan County in 2006. All the 17 microsatellite markers exhibited to be polymorphic in wild populations, yet only six of them were polymorphic in F20 and four polymorphic in F22. Overall 64 alleles were detected in the wild population, and the number of alleles per locus ranged front 2 to 6. But in HAN, only I or 2 alleles Could be detected in each locus, while totally 26 and 21 alleles were found in F20 and F22, respectively. The average homozygosities of these microsatellite loci were 91.96%, 86.18% and 46.84% in F22, F20 and wild population, respectively. The average heterozygosity was 0.5744 in wild population, significantly higher than those of F22 and F20, which showed its high levels of genetic diversity. The average polymorphism information content was 0.5252, 0.3838 and 0.3837 in wild population, F20 and F22, respectively. Therefore, in contrast to wild Population, the high homozygosity and low heterozygosity were found in inbred HAN strain. Among all populations, the genetic similarity index between F20 and F22 was the largest one, which showed the closest genetic distance and the nearest relationship between them. The genetic distance between wild population and F20 was larger than one between F20 and F22, and smaller than one between wild population and F22. On the whole, the present study indicated that genetic diversity of inbred strain was much lower than wild Population, and high genetic purity resulted front long-lime inbreeding was existed in HAN strain. Microsatellite markers were sensitive and effective methods for monitoring genetic quality of laboratory fish. The HAN strain maintained by brother-sister mating should be periodically monitored by microsatellite markers for the Unpurified loci needed to be homozygosis.